BLASTP 2.2.26 [Sep-21-2011]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= 005200
         (709 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|1Q57|A Chain A, The Crystal Structure Of The Bifunctional Primase-helicase
           Of Bacteriophage T7
 pdb|1Q57|B Chain B, The Crystal Structure Of The Bifunctional Primase-helicase
           Of Bacteriophage T7
 pdb|1Q57|C Chain C, The Crystal Structure Of The Bifunctional Primase-helicase
           Of Bacteriophage T7
 pdb|1Q57|D Chain D, The Crystal Structure Of The Bifunctional Primase-helicase
           Of Bacteriophage T7
 pdb|1Q57|E Chain E, The Crystal Structure Of The Bifunctional Primase-helicase
           Of Bacteriophage T7
 pdb|1Q57|F Chain F, The Crystal Structure Of The Bifunctional Primase-helicase
           Of Bacteriophage T7
 pdb|1Q57|G Chain G, The Crystal Structure Of The Bifunctional Primase-helicase
           Of Bacteriophage T7
          Length = 503

 Score = 66.2 bits (160), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 113/474 (23%), Positives = 181/474 (38%), Gaps = 75/474 (15%)

Query: 258 RNGKLVNCKYRDFNKKFWQEKD-TEKVFYGLDDIEGESDIIIVEGEMDKLSMEEAGFLNC 316
           +NG +V+ K RD +K F           +G     G   I++ EGE+D L++ E      
Sbjct: 51  QNGNIVSQKVRDKDKNFKTTGSHKSDALFGKHLWNGGKKIVVTEGEIDMLTVMELQDCKY 110

Query: 317 VSVPDGAPSSVSKKNVPSEEQDTKYQYLWNCKMYLKQASRIILATDGDPPGQALAEELAX 376
             V  G  +S +KK   +  +            Y  Q  +IIL  D D  G+   EE A 
Sbjct: 111 PVVSLGHGASAAKKTCAANYE------------YFDQFEQIILMFDMDEAGRKAVEEAAQ 158

Query: 377 XXXXXXXXXXXXPKKNDVDHFKDANEVLMYLGPGALKEVVENAELY---PIMGLFNFRDY 433
                       P        KDANE  +      + E V NA  +    ++   + R+ 
Sbjct: 159 VLPAGKVRVAVLP-------CKDANECHLNGHDREIMEQVWNAGPWIPDGVVSALSLRER 211

Query: 434 FDEIDAYYHRTSGDEFGIS-TGWRALNE-LYNVLPGELTIVTGVPNSGKSEWIDALICNI 491
             E     H +S +  G+  +G   +N+       GE+ +VT       S ++       
Sbjct: 212 IRE-----HLSSEESVGLLFSGCTGINDKTLGARGGEVIMVTSGSGMVMSTFVRQQALQW 266

Query: 492 NEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFEANYGGSAERMTVE--EFEQGKAWLS 549
               G K  L  +E  V E A  L+  H +    +++   S +R  +E  +F+Q   W  
Sbjct: 267 GTAMGKKVGLAMLEESVEETAEDLIGLHNRVRLRQSD---SLKREIIENGKFDQ---WFD 320

Query: 550 NTF---------SLIRCENDSLPSIKWVLDLAKAAVLRHGVRGLVIDPYNELDHQRPV-- 598
             F         S    E D L        LAK A +R G+   VI     LDH   V  
Sbjct: 321 ELFGNDTFHLYDSFAEAETDRL--------LAKLAYMRSGLGCDVI----ILDHISIVVS 368

Query: 599 ---SQTETEYVSQMLTMVKRFAQHHACHVWFVAHPR-----QLHNWVGEPPNLYDISGSA 650
                 E + +  ++T +K FA+     +  + H +     + H   G P ++ D+ GS 
Sbjct: 369 ASGESDERKMIDNLMTKLKGFAKSTGVVLVVICHLKNPDKGKAHE-EGRPVSITDLRGSG 427

Query: 651 HFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRNKVVGTIGEA-FLSYNRVTG 703
                 D  I + RN+  +   +    V VR ++ +  G  G A ++ YN+ TG
Sbjct: 428 ALRQLSDTIIALERNQQGDMPNL----VLVRILKCRFTGDTGIAGYMEYNKETG 477


>pdb|1E0J|A Chain A, Gp4d Helicase From Phage T7 Adpnp Complex
 pdb|1E0J|B Chain B, Gp4d Helicase From Phage T7 Adpnp Complex
 pdb|1E0J|C Chain C, Gp4d Helicase From Phage T7 Adpnp Complex
 pdb|1E0J|D Chain D, Gp4d Helicase From Phage T7 Adpnp Complex
 pdb|1E0J|E Chain E, Gp4d Helicase From Phage T7 Adpnp Complex
 pdb|1E0J|F Chain F, Gp4d Helicase From Phage T7 Adpnp Complex
 pdb|1E0K|A Chain A, Gp4d Helicase From Phage T7
 pdb|1E0K|B Chain B, Gp4d Helicase From Phage T7
 pdb|1E0K|C Chain C, Gp4d Helicase From Phage T7
 pdb|1E0K|D Chain D, Gp4d Helicase From Phage T7
 pdb|1E0K|E Chain E, Gp4d Helicase From Phage T7
 pdb|1E0K|F Chain F, Gp4d Helicase From Phage T7
          Length = 289

 Score = 49.7 bits (117), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 65/259 (25%), Positives = 104/259 (40%), Gaps = 45/259 (17%)

Query: 467 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFE 526
           GE+ +VT     GKS ++           G K  L  +E  V E A  L+  H +    +
Sbjct: 45  GEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEESVEETAEDLIGLHNRVRLRQ 104

Query: 527 ANYGGSAERMTVE--EFEQGKAWLSNTF---------SLIRCENDSLPSIKWVLDLAKAA 575
           ++   S +R  +E  +F+Q   W    F         S    E D L        LAK A
Sbjct: 105 SD---SLKREIIENGKFDQ---WFDELFGNDTFHLYDSFAEAETDRL--------LAKLA 150

Query: 576 VLRHGVRGLVIDPYNELDHQRPVSQT-----ETEYVSQMLTMVKRFAQHHACHVWFVAHP 630
            +R G+   VI     LDH   V        E + +  ++T +K FA+     +  + H 
Sbjct: 151 YMRSGLGCDVII----LDHISIVVSASGESDERKMIDNLMTKLKGFAKSTGVVLVVICHL 206

Query: 631 R-----QLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRN 685
           +     + H   G P ++ D+ GS       D  I + RN+  +   +    V VR ++ 
Sbjct: 207 KNPDKGKAHEE-GRPVSITDLRGSGALRQLSDTIIALERNQQGDMPNL----VLVRILKC 261

Query: 686 KVVGTIGEA-FLSYNRVTG 703
           +  G  G A ++ YN+ TG
Sbjct: 262 RFTGDTGIAGYMEYNKETG 280


>pdb|1CR0|A Chain A, Crystal Structure Of The Helicase Domain Of The Gene4
           Protein Of Bacteriophage T7
 pdb|1CR1|A Chain A, Crystal Structure Of The Helicase Domain Of The Gene 4
           Protein Of Bacteriophage T7: Complex With Dttp
 pdb|1CR2|A Chain A, Crystal Structure Of The Helicase Domain Of The Gene 4
           Protein Of Bacteriophage T7: Complex With Datp
 pdb|1CR4|A Chain A, Crystal Structure Of The Helicase Domain Of The Gene 4
           Protein Of Bacteriophage T7: Complex With Dtdp
          Length = 296

 Score = 49.7 bits (117), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 65/259 (25%), Positives = 104/259 (40%), Gaps = 45/259 (17%)

Query: 467 GELTIVTGVPNSGKSEWIDALICNINEHAGWKFVLCSMENKVREHARKLLEKHIKKPFFE 526
           GE+ +VT     GKS ++           G K  L  +E  V E A  L+  H +    +
Sbjct: 35  GEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEESVEETAEDLIGLHNRVRLRQ 94

Query: 527 ANYGGSAERMTVE--EFEQGKAWLSNTF---------SLIRCENDSLPSIKWVLDLAKAA 575
           ++   S +R  +E  +F+Q   W    F         S    E D L        LAK A
Sbjct: 95  SD---SLKREIIENGKFDQ---WFDELFGNDTFHLYDSFAEAETDRL--------LAKLA 140

Query: 576 VLRHGVRGLVIDPYNELDHQRPV-----SQTETEYVSQMLTMVKRFAQHHACHVWFVAHP 630
            +R G+   VI     LDH   V        E + +  ++T +K FA+     +  + H 
Sbjct: 141 YMRSGLGCDVI----ILDHISIVVSASGESDERKMIDNLMTKLKGFAKSTGVVLVVICHL 196

Query: 631 R-----QLHNWVGEPPNLYDISGSAHFINKCDNGIVIHRNRDPEAGPIDRVQVCVRKVRN 685
           +     + H   G P ++ D+ GS       D  I + RN+  +   +    V VR ++ 
Sbjct: 197 KNPDKGKAHE-EGRPVSITDLRGSGALRQLSDTIIALERNQQGDMPNL----VLVRILKC 251

Query: 686 KVVGTIGEA-FLSYNRVTG 703
           +  G  G A ++ YN+ TG
Sbjct: 252 RFTGDTGIAGYMEYNKETG 270


>pdb|1NUI|A Chain A, Crystal Structure Of The Primase Fragment Of Bacteriophage
           T7 Primase- Helicase Protein
 pdb|1NUI|B Chain B, Crystal Structure Of The Primase Fragment Of Bacteriophage
           T7 Primase- Helicase Protein
          Length = 255

 Score = 38.1 bits (87), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 50/191 (26%), Positives = 75/191 (39%), Gaps = 24/191 (12%)

Query: 229 RLISAETLRRNRV-MQKRHGHEVVIAFPYWRNGKLVNCKYRDFNKKFWQEKDTEK-VFYG 286
           R IS ET ++    + K  G    +A    +NG +V+ K RD +K F      +    +G
Sbjct: 84  RGISKETCQKAGYWIAKVDGVMYQVADYRDQNGNIVSQKVRDKDKNFKTTGSHKSDALFG 143

Query: 287 LDDIEGESDIIIVEGEMDKLSMEEAGFLNCVSVPDGAPSSVSKKNVPSEEQDTKYQYLWN 346
                G   I++ EGE+D L++ E        V  G  +S +KK   +  +         
Sbjct: 144 KHLWNGGKKIVVTEGEIDMLTVMELQDCKYPVVSLGHGASAAKKTCAANYE--------- 194

Query: 347 CKMYLKQASRIILATDGDPPGQALAEELAXXXXXXXXXXXXXPKKNDVDHFKDANEVLMY 406
              Y  Q  +IIL  D D  G+   EE A             P        KDANE  + 
Sbjct: 195 ---YFDQFEQIILMFDMDEAGRKAVEEAAQVLPAGKVRVAVLP-------CKDANECHL- 243

Query: 407 LGPGALKEVVE 417
              G  +E++E
Sbjct: 244 --NGHDREIME 252


>pdb|2VYE|A Chain A, Crystal Structure Of The Dnac-Ssdna Complex
 pdb|2VYE|B Chain B, Crystal Structure Of The Dnac-Ssdna Complex
 pdb|2VYF|A Chain A, Crystal Structure Of The Dnac
 pdb|2VYF|B Chain B, Crystal Structure Of The Dnac
          Length = 454

 Score = 35.8 bits (81), Expect = 0.095,   Method: Compositional matrix adjust.
 Identities = 63/281 (22%), Positives = 116/281 (41%), Gaps = 27/281 (9%)

Query: 434 FDEIDAYYHRTSGDEFGISTGWRALNELYNVLP-GELTIVTGVPNSGKSEWIDALICNIN 492
           +D I+  ++R +GD  GI TG+  L+ + +     +L IV   P+ GK+ +   +  N+ 
Sbjct: 170 YDNIEMLHNR-NGDITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVA 228

Query: 493 EHAGWKFVLCSMENKVREHARKLL--EKHIKKPFFEANYGGSAERMTVEE---FEQGKAW 547
                   + S+E   ++   ++L  E +I              ++T E+          
Sbjct: 229 TKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTG------KLTPEDWGKLTMAMGS 282

Query: 548 LSNTFSLIRCENDSLPSIKWVLDLAKAAVLRH--GVRGLVIDPYNELDHQRPVSQTETEY 605
           LSN    I    D  PSI+     AK   L+   G+  +VID    +       +   + 
Sbjct: 283 LSNAGIYI----DDTPSIRVSDIRAKCRRLKQESGLGMVVIDYLQLIQGSGRNRENRQQE 338

Query: 606 VSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR 664
           VS++   +K  A+     V  ++   R +     + P + D+  S       D    ++R
Sbjct: 339 VSEISRSLKALARELEVPVIALSQLSRSVEQRQDKRPMMSDLRESGSIEQDADIVAFLYR 398

Query: 665 ----NRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFL-SYNR 700
               N+D E    + +++ + K RN  VGT+  AF+  YN+
Sbjct: 399 DDYYNKDSENK--NIIEIIIAKQRNGPVGTVQLAFIKEYNK 437


>pdb|2R6A|A Chain A, Crystal Form Bh1
 pdb|2R6A|B Chain B, Crystal Form Bh1
 pdb|2R6E|A Chain A, Crystal Form B2
 pdb|2R6E|B Chain B, Crystal Form B2
 pdb|2R6C|A Chain A, Crystal Form Bh2
 pdb|2R6C|B Chain B, Crystal Form Bh2
 pdb|2R6C|C Chain C, Crystal Form Bh2
 pdb|2R6C|D Chain D, Crystal Form Bh2
 pdb|2R6C|E Chain E, Crystal Form Bh2
 pdb|2R6C|F Chain F, Crystal Form Bh2
 pdb|2R6D|A Chain A, Crystal Form B1
 pdb|2R6D|B Chain B, Crystal Form B1
 pdb|2R6D|C Chain C, Crystal Form B1
 pdb|2R6D|D Chain D, Crystal Form B1
 pdb|2R6D|E Chain E, Crystal Form B1
 pdb|2R6D|F Chain F, Crystal Form B1
 pdb|4ESV|A Chain A, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|B Chain B, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|C Chain C, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|D Chain D, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|E Chain E, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|F Chain F, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|G Chain G, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|H Chain H, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|I Chain I, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|J Chain J, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|K Chain K, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
 pdb|4ESV|L Chain L, A New Twist On The Translocation Mechanism Of Helicases
           From The Structure Of Dnab With Its Substrates
          Length = 454

 Score = 35.4 bits (80), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 63/281 (22%), Positives = 115/281 (40%), Gaps = 27/281 (9%)

Query: 434 FDEIDAYYHRTSGDEFGISTGWRALNELYNVLP-GELTIVTGVPNSGKSEWIDALICNIN 492
           +D I+  ++R  G+  GI TG+  L+ + +     +L IV   P+ GK+ +   +  N+ 
Sbjct: 170 YDNIEMLHNR-DGEITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVA 228

Query: 493 EHAGWKFVLCSMENKVREHARKLL--EKHIKKPFFEANYGGSAERMTVEE---FEQGKAW 547
                   + S+E   ++   ++L  E +I              ++T E+          
Sbjct: 229 TKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTG------KLTPEDWGKLTMAMGS 282

Query: 548 LSNTFSLIRCENDSLPSIKWVLDLAKAAVLRH--GVRGLVIDPYNELDHQRPVSQTETEY 605
           LSN    I    D  PSI+     AK   L+   G+  +VID    +       +   + 
Sbjct: 283 LSNAGIYI----DDTPSIRVSDIRAKCRRLKQESGLGMIVIDYLQLIQGSGRSKENRQQE 338

Query: 606 VSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVGEPPNLYDISGSAHFINKCDNGIVIHR 664
           VS++   +K  A+     V  ++   R +     + P + DI  S       D    ++R
Sbjct: 339 VSEISRSLKALARELEVPVIALSQLSRSVEQRQDKRPMMSDIRESGSIEQDADIVAFLYR 398

Query: 665 ----NRDPEAGPIDRVQVCVRKVRNKVVGTIGEAFL-SYNR 700
               N+D E    + +++ + K RN  VGT+  AF+  YN+
Sbjct: 399 DDYYNKDSENK--NIIEIIIAKQRNGPVGTVQLAFIKEYNK 437


>pdb|3BH0|A Chain A, Atpase Domain Of G40p
          Length = 315

 Score = 33.9 bits (76), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 30/120 (25%), Positives = 55/120 (45%), Gaps = 3/120 (2%)

Query: 580 GVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVG 638
           G R +V+  Y +L      + + T  +SQ+   +K+ A+     V  ++   RQ+     
Sbjct: 180 GKRVIVMIDYLQLLEPAKANDSRTNQISQISRDLKKMARELDVVVIALSQLSRQVEQRQD 239

Query: 639 EPPNLYDISGSAHFINKCDNGIVIHRNR--DPEAGPIDRVQVCVRKVRNKVVGTIGEAFL 696
           + P L D+  S       D    ++R+   D E+   + V+V + K R+  VGT+  AF+
Sbjct: 240 KRPMLSDLRESGQLEQDADIIEFLYRDDYYDKESESKNIVEVIIAKHRDGPVGTVSLAFI 299


>pdb|3BGW|A Chain A, The Structure Of A Dnab-like Replicative Helicase And Its
           Interactions With Primase
 pdb|3BGW|B Chain B, The Structure Of A Dnab-like Replicative Helicase And Its
           Interactions With Primase
 pdb|3BGW|C Chain C, The Structure Of A Dnab-like Replicative Helicase And Its
           Interactions With Primase
 pdb|3BGW|D Chain D, The Structure Of A Dnab-like Replicative Helicase And Its
           Interactions With Primase
 pdb|3BGW|E Chain E, The Structure Of A Dnab-like Replicative Helicase And Its
           Interactions With Primase
 pdb|3BGW|F Chain F, The Structure Of A Dnab-like Replicative Helicase And Its
           Interactions With Primase
          Length = 444

 Score = 33.9 bits (76), Expect = 0.35,   Method: Compositional matrix adjust.
 Identities = 30/120 (25%), Positives = 55/120 (45%), Gaps = 3/120 (2%)

Query: 580 GVRGLVIDPYNELDHQRPVSQTETEYVSQMLTMVKRFAQHHACHVWFVAH-PRQLHNWVG 638
           G R +V+  Y +L      + + T  +SQ+   +K+ A+     V  ++   RQ+     
Sbjct: 309 GKRVIVMIDYLQLLEPAKANDSRTNQISQISRDLKKMARELDVVVIALSQLSRQVEQRQD 368

Query: 639 EPPNLYDISGSAHFINKCDNGIVIHRNR--DPEAGPIDRVQVCVRKVRNKVVGTIGEAFL 696
           + P L D+  S       D    ++R+   D E+   + V+V + K R+  VGT+  AF+
Sbjct: 369 KRPMLSDLRESGQLEQDADIIEFLYRDDYYDKESESKNIVEVIIAKHRDGPVGTVSLAFI 428


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.319    0.135    0.413 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,892,274
Number of Sequences: 62578
Number of extensions: 846566
Number of successful extensions: 1971
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1965
Number of HSP's gapped (non-prelim): 8
length of query: 709
length of database: 14,973,337
effective HSP length: 106
effective length of query: 603
effective length of database: 8,340,069
effective search space: 5029061607
effective search space used: 5029061607
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)